Variant report

Variant	rs7980681
Chromosome Location	chr12:105245316-105245317
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1002803	0.85[EUR][1000 genomes]
rs1038968	0.84[EUR][1000 genomes]
rs10746008	0.81[ASN][1000 genomes]
rs1155994	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1316594	0.91[EUR][1000 genomes]
rs1389609	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1389612	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1565813	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1565815	0.90[EUR][1000 genomes]
rs2047124	0.84[EUR][1000 genomes]
rs2141248	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2245927	0.91[EUR][1000 genomes]
rs2245931	0.91[EUR][1000 genomes]
rs2248012	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2453157	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2453158	0.91[EUR][1000 genomes]
rs2453160	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2453161	0.80[EUR][1000 genomes]
rs2453166	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2453167	0.91[EUR][1000 genomes]
rs2453168	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2463016	0.91[EUR][1000 genomes]
rs2463017	0.91[EUR][1000 genomes]
rs2463018	0.86[EUR][1000 genomes]
rs2463025	0.91[EUR][1000 genomes]
rs2463429	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2463431	0.84[EUR][1000 genomes]
rs2463432	0.90[EUR][1000 genomes]
rs2463433	0.91[EUR][1000 genomes]
rs2463440	0.80[EUR][1000 genomes]
rs2468083	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2468089	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2468090	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2468092	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2468099	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2468100	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2468105	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2468340	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2565167	0.91[EUR][1000 genomes]
rs2642110	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2642116	0.91[EUR][1000 genomes]
rs2730291	0.83[EUR][1000 genomes]
rs2730295	0.85[EUR][1000 genomes]
rs2731030	0.85[EUR][1000 genomes]
rs4334113	0.86[ASN][1000 genomes]
rs4388976	0.87[ASN][1000 genomes]
rs4393404	0.86[ASN][1000 genomes]
rs6539167	0.84[EUR][1000 genomes]
rs6539170	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539171	0.81[ASN][1000 genomes]
rs7135015	0.84[ASN][1000 genomes]
rs7847	0.86[EUR][1000 genomes]
rs7967503	0.85[ASN][1000 genomes]
rs9669207	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv899497	chr12:105155291-105247010	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv899498	chr12:105173598-105461620	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7980681	CHST11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105220800-105260600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:105222000-105258400	Weak transcription	Duodenum Mucosa	Duodenum
3	chr12:105222000-105258600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:105222200-105258800	Weak transcription	Pancreas	Pancrea
5	chr12:105229000-105259200	Weak transcription	Placenta	Placenta
6	chr12:105233200-105258600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr12:105236200-105258600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:105237400-105259000	Weak transcription	A549	lung
9	chr12:105238400-105257000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr12:105238400-105260400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr12:105238400-105280000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr12:105239800-105250400	Weak transcription	Adipose Nuclei	Adipose
13	chr12:105240600-105252400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:105240600-105258800	Weak transcription	Aorta	Aorta
15	chr12:105240800-105245800	Weak transcription	Osteobl	bone
16	chr12:105243000-105255800	Weak transcription	Colonic Mucosa	Colon
17	chr12:105243800-105265800	Weak transcription	Fetal Stomach	stomach
18	chr12:105244000-105248600	Weak transcription	Liver	Liver
19	chr12:105245200-105246400	Enhancers	NHDF-Ad	bronchial

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